entimICE FastTrack and Posit – The Ideal Couple for Clinical Research?

By entimo

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The R programming language has become a cornerstone in clinical research due to its extensive range of statistical tools and graphical capabilities. Central to its flexibility and power is the comprehensive ecosystem of packages available through CRAN (Comprehensive R Archive Network), Tidyverse, Pharmaverse, Bioconductor and GitHub. However, managing these packages presents both significant challenges and notable benefits for researchers.

Posit (formerly known as RStudio) is a comprehensive integrated development environment (IDE) for R, offering a range of tools and features that significantly enhance R package management. Its benefits in the context of clinical research are particularly pronounced due to the complex and sensitive nature of the data and analyses involved.

entimICE FastTrack is an integrated Clinical Data Repository (CDR) and Statistical Computing Environment (SCE) platform, designed and built with decades of experience from both entimo and its industry customers. It provides effortless regulatory compliance, while enabling researchers to manage tasks and monitor progress towards successful submissions.

Bringing entimICE FastTrack and Posit together pairs two great systems, and helps researchers make the most of R’s powerful capabilities.

Challenges of using R

Because it is such a powerful tool, R can pose challenges for programmers and scientists who want to get the most out of it. Below are five common ones – read further to find out how Posit and entimICE FastTrack work together to help overcome them.

Version Control and Reproducibility

One of the most pressing challenges in clinical research is ensuring reproducibility. Because R packages are frequently updated, changes in functions or dependencies can lead to discrepancies in research results over time. Maintaining consistent versions of packages across different stages of research and among different collaborators is crucial, but can be difficult without rigorous version control practices.

Dependency Management

Many R packages rely on other packages, creating complex dependency chains. A single update in one package can potentially disrupt the functionality of others. This interdependency requires careful management to avoid conflicts and ensure that all necessary packages work harmoniously together.

Installation and Compatibility Issues

Installing and configuring R packages can be problematic, particularly when dealing with packages that require compilation or are dependent on system-specific libraries. These issues are amplified in clinical research environments where stringent IT policies and varying operating systems are common.

Documentation and Learning Curve

While the breadth of available packages is a strength, it also presents a learning curve. Not all packages are equally well-documented, and deciphering how to use a package correctly and effectively can be time-consuming. This is particularly important in clinical research, where the accuracy and reliability of analyses are paramount.

Regulatory Compliance

Clinical research is heavily regulated, requiring strict adherence to guidelines for data handling, analysis, and reporting. Ensuring that all R packages used are compliant with these regulations and that their usage is documented and validated is a significant challenge.

Benefits of using R with Posit

Adding the strengths of R to the extended possibilities offered by Posit offers numerous benefits to users in the pharma and research sector. Here are seven concrete advantages – and then keep reading to learn more about how these tools mesh with entimICE FastTrack.

Streamlined Package Installation and Updates - Posit Package Manager (PPM)

PPM provides one or more centralized repositories for R packages, which simplifies the process of finding and installing the correct versions of packages. It offers curated and vetted packages, ensuring that the packages are reliable and reducing the risk of installing malicious or buggy software. PPM supports versioned snapshots, allowing users to install packages as they existed on a specific date, which is crucial for reproducibility. Packages can be maintained within the repository, removing dependencies on external third parties (such as CRAN or GitHub).

Enhanced Reproducibility - Project Environments

Posit allows you to create project-specific libraries where each project can have its own set of packages and versions, avoiding conflicts between projects. Packrat and renv are integrated into Posit, facilitating the creation of isolated, reproducible environments. This ensures that analyses can be reliably reproduced by other researchers or at a later date.

Dependency Management and Tracking

Posit can automatically detect and install package dependencies, ensuring that all required packages and their dependencies are available and compatible. It provides tools to visualize and manage package dependencies, helping to identify and resolve conflicts easily.

User-Friendly and Intuitive Interface

Posit’s user-friendly interface includes features such as point-and-click package installation, updates, and management, making it accessible even for researchers who are not programming experts. Access to package documentation and vignettes directly within the Internal Development Environment helps researchers understand and use packages more effectively.

Enhanced Productivity Features

Posit provides advanced script management features, including syntax highlighting, code completion, and debugging tools, which enhance coding efficiency and reduce errors. For researchers developing their own packages, Posit offers robust development tools, including testing frameworks and build management, both of which streamline the development process.

Compliance and Security

PPM can restrict access to certain packages and versions, ensuring that only approved and compliant packages are used in clinical research settings. Posit provides audit trails for package installations and updates, which are essential for regulatory compliance in clinical research.

Community and Support Resources

Posit has a large and active user community that runs forums and discussion groups where researchers can seek help and share knowledge. Posit provides professional support services, which can be invaluable in troubleshooting complex package management issues and ensuring smooth operations in a clinical research environment.

Posit and entimICE FastTrack

Combining Posit and entimICE FastTrack brings together the strengths of both environments, with significant benefits for clinical data analysis and reporting.

Effortless Compliance

entimICE FastTrack ensures effortless compliance and end-to-end traceability for all artifacts, including data, programs, images, and large files such as biomarkers. Integrated version management tracks changes, while pre-configured workflows streamline validation and lifecycle management. Seamless integration with Posit keeps all data and program code changes updated in the repository.

Personalized Computing Environment

entimICE FastTrack's intuitive UI enables users to design custom dashboards and context-specific collections of objects of interest. Interactive visual reports track dependencies from raw data to submission-ready deliverables and monitor study progress. Users can complete all R- and Python-based programming tasks using Posit, which can provide a dedicated repository/execution environment per study to ensure compliance.

Shared or Individual Work Areas

entimICE FastTrack supports collaborative work on clinical data without the need for exporting snapshots or cumbersome check-out/check-in procedures. The data repository provides a single source of truth for all data processing steps. Additionally, users can establish individual work areas for exploratory work.

Ready for Exploratory and Submission Workflows

The system supports both exploratory data analysis using a variety of statistical tools, including Posit, and generating submission-ready deliverables through tightly integrated R functionalities. entimICE FastTrack offers clinical data scientists the freedom to explore where appropriate, alongside strict guidance and conformance where necessary.

Language Agnostic

entimICE FastTrack is truly language-agnostic. While fully supporting R and Python through Posit integration, the system also accommodates other toolsets, including industry-standard SAS, its programming language along with tools like Enterprise Guide or SAS Studio. Integration with SAS Viya is currently in development.

Pairing Up

R package management is a double-edged sword in clinical research. The challenges including version control, dependency management, installation issues, documentation, and regulatory compliance make meticulous planning and management necessary. However, the benefits such as enhanced analytical capabilities, reproducibility and efficiency make R an invaluable asset in clinical research. Effective package management practices are essential to leveraging R's full potential while mitigating the inherent challenges, ultimately contributing to the advancement of clinical research.

Using Posit for R package management in clinical research offers numerous benefits. These include streamlined package installation and updates, enhanced reproducibility, effective dependency management, and a user-friendly interface. Additionally, Posit fosters collaboration, enhances productivity, and provides extensive community and professional support. These features make Posit an invaluable tool for managing R packages, ultimately contributing to more reliable and efficient clinical research practices.

The integration of Posit with entimICE FastTrack allows data scientists and biostatisticians in highly regulated environments to enjoy the best of both worlds: They gain the freedom to use a large variety of R packages for exploratory analysis, while ensuring full compliance during submission runs using an exclusive validated R environment. This powerful combination of two tools significantly enhances clinical data science, leading to faster and more successful submissions.

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